In e6m2 there is a switch in one of the corner areas that does nothing. It doesn't have a trigger line.
A switch near the long stairs cannot be triggered either but it has a trigger line.
The door at the bottom of the long stairs does not open as a result.
Edit1: In e6m6 there is no sapphire rune to be found to unlock too last door. Even using the automap show keys cheat I couldn't see one.
After noclipping my way out, end-of-map screen came. There wasn't an ancients fight.
Edit2: Again in e6m6 in the green key room there are three unknown objects. Green key's name is green key, not emerald rune. Key is only reachable by jumping over the gaps. After taking the key, the newly opened room has seven unknown objects. In the secret room there are three unknown objects. In the room with a blood walled inner room, there are nine unknown objects. I am writing these as I play but I wish I just wrote e6m6 was full of unknown objects
Edit3: In e6m3 after getting through the blue door, despite clearing and and triggering everything in side doors, I coulndn't open the door that leads the way across.
Edit4: End-of-map screen came again at end of e6m3. Also all bosses, Baal included, are very easy to kill.
Edit5: Walls of e8m1 are transparent looking from outside. You can walk through all the windows there. Also secret door doesn't open. Some doors related to their respective switches are already open.
Edit 6: You can't switch back to Kalim's Will and it doesn't seem like a good weapon.
Also there are many texture transparency problems beginning by Kurast to the end of the game but they don't affect gameplay so I didn't catalogued them.